DNA Origami: Folding DNA into Tiny Shapes--Dr Guillermo Acuña, University of Fribourg

A revolution in fabricating DNA into useful objects is underway and Dr. Guillermo Acuña of the University of Fribourg in Switzerland is right in the middle of it. In a talk sponsored by Telluride Science, he laid out a world of possibilities; tiny drug delivery devices, nano sensors to detect disease, tiny traps to catch cancer cells. His presentation, in Mountain Village, Colorado, was moderated by veteran broadcast journalists Judy Muller and George Lewis. Our sponsors are Alpine Bank and the Telluride Mountain Village Owners' Association.

Transcript

Science Straight Up

Season 6, Episode 5

Dr. Guillermo Acuña—University of Fribourg

Moderators: George Lewis and Judy Muller

“Folding DNA Into Tiny Shapes”

(theme music)

GEORGE: From Telluride Science, it’s Science Straight Up.”

JUDY: And on this episode…

GUILLERMO: Now this was really a revolution. However, it was a rather silent one, in the sense that this technique was very, very challenging to implement.

GEORGE: A revolution in manipulating and folding DNA into useful objects. It’s the stuff of science fiction. Little nano-bots, not made out of plastic or metal but out of DNA, the stuff that that serves as a genetic blueprint for human beings and all living creatures, great and small.

JUDY: This art of folding DNA is known as “DNA origami,” and we’ll get into that in just a moment. Dr. Guillermo Acuña is a full professor at the physics department at the University of Fribourg in Switzerland. He was one of the distinguished participants in this year’s Telluride Science workshops. He spoke to the community in a “Town Talk” put on by Telluride Science.

GUILLERMO: It's a real pleasure and an honor to be to take part in this town talks. It's also my first time here in Telluride, and so far, it has been really, really outstanding. And also, thank you very much for for giving me the chance to talk a little bit about the research that we are currently doing at the University of Fribourg in Switzerland. And indeed, today, I would like to talk a little bit about how we can use DNA to fabricate tiny structures with very defined geometries and architectures.  I would like to start by by this sentence or this phrase, there's plenty of room at the bottom, and this was a line set by Professor Richard Feynman, Nobel Prize winner in 1965 and a phrase that many scientists working of the field have listened to many, many times, and they're probably tired of it, but this was one of the first actual invitations to enter a  new field of physics, to actually study and explore what happens at very, very tiny dimensional scales which are way beyond what we can see with our bare eyes or we can see with, let's say, conventional light microscopy.

GEORGE: He credits the work of the late Dr. Ned Seeman, a biochemist, who, while at a bar in Albany, New York, first envisioned the idea of building DNA structures. Almost sounds like the setup line for a joke. This biochemist walks into a bar and…

GUILLERMO: He was having his beer, and at some moment, there was this picture of Escher called Depth handing on the wall, and he saw it and he thought, I’m going to use DNA to fabricate structures.

JUDY: He’s talking about the famous woodcut print called “Depth” by artist M.C. Escher that has patterns of strange fish with fins on the tops and bottoms of their bodies as well as left and right.

GEORGE: Here’s the late Dr. Seeman on an old YouTube video talking about that eureka moment in the bar.

NED SEEMAN: I went to the bar. I went to the bar intentionally to think about six-armed junctions of DNA. But while I was sitting in the bar, having my beer, I suddenly thought about Escher’s woodcut “Depth” which has fish in it, 3-D arrangement, sorta like jacks.

GEORGE: That was from the Franklin Institute of Chemistry, which awarded Dr. Seeman its chemistry medal in 2016.

GUILLERMO: This was actually the birth of the  first DNA nanotechnology, or synthetic structures fabricated with DNA. And essentially, 10 years ago, he moved to much more complex structures in three dimensions, made of several different of these single stranded DNA that hybridize and create these fascinating structures of nanometer dimensions. Now this was really a revolution. However, it was a rather silent one, in the sense that this technique was very, very challenging to implement.

JUDY: When I heard it was called DNA origami, it caught my attention, because when I was a young girl, I lived in Japan for a time and fell in love with the art of origami. But here, we’re not folding squares of paper into swans, we’re in the nanoverse. .

GUILLERMO: And this nanometer range is where, for example, viruses, proteins and DNA live. And perhaps for us, it's very hard to picture the nanometer range because it's so far compared to the things we daily interact. But you could think, for example, of a human hair if that has a diameter of roughly 100 micrometers.

GEORGE: So, if you had a teeny-weenie measuring tape and measured the diameter of that human hair, then divide that number by 100,000, you’ve got one nanometer. 

JUDY: You’re in a small world and you’ve got a DNA sample, known as a scaffold, that you want to turn into useful objects. How do you do that?  Well, you can’t use tiny tweezers.

(sound of computer booting up)

GEORGE: But there is computer aided design software that will help us do that. We’ve got our DNA scaffold, we’ve got the genetic code for the scaffold, written not in ones and zeros like computer code, but in the letters A, C, T and G that stand for the four building blocks of DNA, known as nucleotide bases.

GUILLERMO: So you pre load your scaffold, and then you essentially draw which shape would you like to have. And this software calculates which are the very small staples that you need later to fold everything.

JUDY: So, using the shape you’ve scanned into the computer, the software spits out a whole batch of new codes that you’ll need to create those DNA fragments called staples. You send those codes--all those A’s, C’s, T’s and G’s—to a DNA fabrication lab and say, “make me a set of these.”

GEORGE: They’ll send you back a batch of tubes with your little DNA staples suspended in liquid that you can mix up with your DNA scaffold. Heat up the mixture, and, Voila! Your custom-designed DNA objects emerge.

JUDY: What makes it work is that the nucleotide bases of DNA—those bulding blocks—like to arrange themselves in a certain fashion. A is attracted to T and C is attracted to G. If you write out the code for the DNA staples in the right way, they’ll gravitate to the places where you want to bend your DNA scaffold.

GUILLERMO: And let's keep in mind, this is done in solution, in a tube, so we can actually fabricate billions of structures at the same time. 

GEORGE: So, what kinds of things do we want to fabricate? Dr. Acuña says there’s experimental work going on to make tiny drug delivery systems that will head for the exact places in the body where they’re needed. And DNA nano-bots that can be used as disease detectives.

GUILLERMO: We use DNA origami as a bio sensor, and here we combine this with fluorescence, and we try to detect DNA or RNA sequences as markers for breast cancer.

GEORGE: He also talked about DNA traps that could be programmed to catch cancer cells.

JUDY: At Dr. Acuña’s town talk, We had a lot of questions and so did the audience.

GEORGE FROM TOWN TALK RECORDING: If we can just review a little bit of what you said. Your research involves the chemical blocks that make up DNA. The letters for these nucleotides are A, T, G and C.

JUDY: They get along with each other in a specific way, like A is attracted to T and C has a thing for G. We're trying to sex this up a little bit, just that's how it works.

GEORGE: So are we good so far? 

GUILLERMO: I would say, from from my physics perspective, which is not very deep into biology, that is perfect.

GEORGE: So then you get computer design involved, and you design these little staples that cause larger strands of DNA to fold in a certain way. With so many researchers now attracted to this DNA origami for various purposes. Are there? Is there a lot of sharing of discoveries in this field? Or is it highly competitive, or both?

GUILLERMO: I haven't. Say, in most communities, most scientific communities I have been working on, people tend to be very open about things. When one typically published something in a higher rank journal. One wants to put as much information as possible, because otherwise you don't like other people to try to reproduce your work and not not be able to do so, because then, you know, it looks a bit not reproducible, and that's that's not nice. So most people would actually file for a patent to essentially protect whatever they have found. But then they would be very open, and they will really explain, essentially, they will include a protocol, a very detailed protocol, on how to reproduce their findings.

JUDY: You mentioned that you work basically in basic research, fundamental science, and which is so important in your field. But do you think it gets short shrift from funders? I mean, everybody's always looking for grants and help do funders really understand the value of basic research?

GUILLERMO: Of course, people always want to have some sort of return of investment in the short term. And this is really a little bit against scientific research, in the sense that history gives us so many examples of things that at the beginning, didn't seem to have any application, and today they are vital for us. And I think when we talked there was this example of the X-rays that were developed by Roentgen in Germany. He really didn't care at all about medicine or anything related to an application. And I don't think any person in the developed world dies without having taken at least one X-ray image. Although at the time, people were thinking, Okay, what is this useful for?

GEORGE: You talked about some of the applications in medicine, such as drug delivery systems or traps for cancer cells. Can you elucidate on that a little more?

GUILLERMO: Yes. So for example, at least in my case, one relatively straightforward thing to implement is bio essays based on the DNA origami technique that specifically recognize DNA or RNA sequence, which can be used as markers for different disease or or for circulating tumor cancer, tumor cells. So we have a collaboration with the Department of Medicine and cancer research, and we detect short fragments of DNA that essentially get cut out from from cancer tumor cells. For example, of course, there's a lot of research into apply this for medical application. There are several groups and a couple of startups I have shown, and I know of another one that we're also we're also consulting, yes,

GEORGE: If I may follow up, what are some of those promising applications that you see?

GUILLERMO: I don't know. I mean, I'm always very cautious with that, because, you know, some things might seem promising, and then they never work, or something on my get stuck, and then there is some sort of breakthrough idea. I think it's based on what has been already published. I think bio sensing, or DNA sensing, using DNA origami, has been extensively used. So I would say that that might become a real application in the market sooner than others like DNA sequencing. That there are a couple of startups that are working on that, but this might take longer since they have just started, and I can see some some challenges along the way.

JUDY: You quoted Richard Feynman and  a big fan and saying that there's a lot of room at the bottom, yes, the beginning of research. How have you seen this explode? It's pretty new, decade to two decades old, right? Yes. Have you seen it just grow exponentially, or was there a lot of room at the bottom when you started?

GUILLERMO: Okay, so the first thing I want to say is that I would never put that phrase in a scientific talk, because most scientists are extremely tired of seeing that it's like a no go. You cannot put that phrase in a scientific talk. 

GEORGE: And yet, you did.

GUILLERMO: And I'm very worried that I see some scientific faces. Don't worry about they know what I mean. They would also never do it. Now it is true that at the time, Richard Feynman said that there were very few techniques to actually look into the nanometer world 38:34 And so yes, I, to some extent, I witnessed a revolution. It had probably started a bit before. Nevertheless, I would say it's really increased exponentially.

GEORGE: Okay, let's open it up to questions from the audience.

JUDY:    And a reminder, a question is a sentence with a question mark at the end, preferably brief. Thank you. JUDY: 39:42 And a reminder, a question is a sentence with a question mark at the end, preferably brief. Thank you. 

QUESTION FROM AUDIENCE: My question is, what is the status of patenting of this technology. Are there no patents? Is there a master patent on the origami technique? Are there lots of patents on different applications?

GUILLERMO: The main patent is going to run out soon. It was 20 years ago, but there are many, many, many patents. So this really started a revolution in the field. And I can say, currently there are, I would say, hundreds of groups working on this technique, in us, hundreds of groups working in Europe, hundreds of groups working in China. And these people, of course, develop or come with very technological developments that are willing to patent. So there are a fair share of patents in this field.

QUESTION FROM AUDIENCE: My question is, how does the folding stop?

GUILLERMO: Essentially, it is already encoded where when to stop, because there's a certain amount of staples that will hybridize with this very long one. And once this is done, it's done. I mean, there is no further folding. So that's the beauty of it, or it's already the information is already in that DNA strand. It already knows when, when to stop. 

JUDY: One questioner wondered about imperfections in the process. What if the staples don’t do their job and fail to fold the DNA the way they’re designed. Dr. Acuña said basically, you make a lot of excess staples so your chances of success go way up.

GUILLERMO: So another advantage of this technique, and another reason why this is relatively easy to implement, is that one has a high excess of staples, or one can have a high excess of staples to scaffold. So I mean the higher excess you use, the higher yield of perfectly folded structures that you're going to get. We typically use a tenfold excess of staples. Some people use 100. People have a lot of funding, and some people use one or two times excess. And yeah, of course, later you need to filter that and discharge that.

GEORGE: Dr. Acuña briefly mentioned that some of his research involved photons—light particles—and how they might react with DNA structures in the nano universe.  An audience member wanted to know more about that.

QUESTION FROM AUDIENCE: So this is basically a physical thing that you're working with, and it, does it combine chemically with things, or does it just in the nanophotonics that you're doing? Would it give a reflection, if you had the right shape and it was hit by a chemical. So could it be used for sensors and that kind of thing?

GUILLERMO: So, in principle, DNA does not really interact with light in in the visible spectral range. So if you throw light to DNA, they don't they don't talk to each other. Light, just go through it. So now in principle, these structures will not really reflect light. Now what one can do is which is related to what I work on. One can put different things onto these structures. One can put, for example, gold nanoparticles, so some very, very small nanoparticles that actually interact with light. And you could use that to have surfaces that reflect light. And there are some, at least, papers that discuss, you know, labeling, functionalizing windows with this kind of technique to, you know, tint the glass, or have different optical properties to cool down houses or these kind of things. This, at this stage, is a bit science fiction, but there are some people looking into such applications.

JUDY: I'm just curious about the very term origami being adapted for this science. Do you think that that helps explain it to people who might be okay, we got DNA staples and we've got but if you say,

GUILLERMO: I think maybe for the audience to answer that, I mean, like, do you think it helped if I used origami to call it origami, does it just could?

JUDY: Yeah, most people think so.

GEORGE: There was a question about whether DNA origami could be used in computers to replace conventional silicon chips.

GUILLERMO: There are some groups mine included that use this DNA origami to position things that are called carbon nanotubes, that have a very high electric mobility. And the idea here is to kind of replace standard logical gates, essentially done by electrons, by electronic circuits in silicon. So there are quite some initiatives to use DNA origami to position elements, to make nano circuits and logical gates. And this is one of the things I'm working on, and there's been tremendous developments in this field in Harvard.

JUDY: Mark Kozak, the executive director and CEO of Telluride Science, had a question.

MARK: What other besides this approach to building nano materials? What other techniques are used to build nano materials? Like, why would you necessarily use this approach to build something or framework versus another approach, and were what would be an example of another approach?

GUILLERMO: There's essentially another family of techniques that they are called top down, in which you can essentially write on a surface. And instead of using a pencil, you use a beam of electrons that are accelerated to extremely high velocities. They impinge onto a surface, and they have a very, very tiny focus. And with this, you can write very precisely, and you can fabricate structures in the nanometer range. This is an incredible technique to fabricate many things. This is, as I mentioned, relatively expensive. These machines cost a lot of money. They also need to be inside what we call a clean room, because every dust particle, hair and so on, affects so they have a lot of running costs to maintain. And to be fairly honest, the group where I work in in the north of Germany, they didn't have, we didn't have access to such a clean room. So think it was another advantage. So yes, there are plenty of other techniques from top down, but also bottom up. Instead of using DNA, some people use proteins or other compounds to self-assemble. Perhaps, what I think is the main advantage of this is that it is extremely I mean, it is cost efficient. One only needs a PCR machine that is something that costs something around $5,000 and it's fairly easy to fabricate. Again, I am a physicist by training, I was never entering a chem lab before my post doc. And I mean, not now, but essentially 10 years ago, I could fabricate these structures every other day, whereas other techniques are very challenging and one needs a lot of training. And having this open-source software, one can also, you know, just pretty much draw anything, and then the software, okay, well, that will check if it is really doable. But if it is doable, I would say maybe in two to three weeks, you have your your structure running. But yes, of course, there are other techniques that have some pros and cons. And I mean, this is not the only way, and this works very good for some things and other techniques. For example, you want to have an array of very, very defined structures, you will probably use top-down approaches.

JUDY: That is all the time we have this evening. (applause) Thanks to all of you for coming and to Telluride science, for making these town talks possible. And let's give another big

hand to Dr Thank you. Thank you. Thank you very

much.

JUDY AND GEORGE IN UNISON: And a big had to Doctor Guillermo Acuña!

( Applause) 

(THEME MUSIC) 

JUDY: And a special thank you to the sponsors who help make all this possible, Alpine Bank and the Telluride Mountain Village Owners’ Association.

GEORGE: Dr Acuña was recorded before a live audience at the Telluride Conference Center in Mountain Village. A big shout-out to our audio folks, Dean Rolley and Vicki Phelps.

JUDY: Mark Kozak is the executive director and CEO of Telluride Science and Cindy Fusting is managing director and CFO. Sara Friedberg is Lodging and Operations Manager and Annie Carlson is Director of Donor Relations.

GEORGE: If YOU want to donate to the cause, go to Telluride Science-dot-ORG. That’s also where you can find our podcasts. And on your podcast apps like Spotify or Apple, look for “Science Straight up.” I’m George Lewis.

JUDY: And I’m Judy Muller, inviting you to join us next time on “Science Straight Up.”

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