Designer DNA
Watch the Dance Your PhD contest winning video.
By Tyler Irving
It’s not quite a needle in a haystack, but finding a patch of potentially toxic mold in an entire field’s worth of grain is a task of comparable complexity. Fortunately, modern technology allows for the creation of tiny strands of DNA called aptamers, which selectively bind almost any molecule, from toxins in the aforementioned mold, to neurotransmitters like dopamine.
But can these biochemical curiosities be translated into viable commercial products? Maria DeRosa of Carleton University is palpably optimistic that they can. If you don't believe us, just check out her dance moves.
ACCN: What is an aptamer?
M.D.: It’s basically a small synthetic piece of DNA or RNA, and it folds up into a nano-scale shape. Something about that shape allows it to bind to another molecule. That other molecule could be something small, like a drug, it could be something bigger, like a protein, or very big, like a virus or a bacterium, but something about that shape allows it to interact with high affinity and usually very good specificity. And then we can use that aptamer in other types of applications that are related to this biorecognition event.
ACCN: How is it different from an antibody?
M.D.: It’s very similar, and a lot of times people will call aptamers nucleic acid antibodies, because it’s a similar idea. It still relies on its shape for bonding, but it’s based on nucleic acids instead of proteins. So just because of its different composition, it has different kinds of properties that allow it to be useful in other places that antibodies aren’t always useful. [Antibodies] are built out of proteins, and proteins are unstable to things like heat, changes in pH and changes in salt concentration. If you’re in one of those applications, you may have a problem. Aptamers, on the other hand, are more stable to temperature changes. If they do unfold and they lose their shape, you can get them back without losing the binding affinity, which is different from antibodies. If you fry an egg, you can’t get it back to the yolk, right?
ACCN: How do you make an aptamer?
M.D.: The field isn’t at the point where we can say, okay, here’s a target, and here’s what I want the aptamer to look like, so let’s design an aptamer. What we have to do instead is a selection. We start off with lots and lots of random pieces of DNA, all sorts of different sequences, which will make all sorts of different shapes. We expose that pool of DNA to the target, and we keep the pieces that bind, and we get rid of the ones that don’t. Usually we start off with something like 1015 different sequences, so a large pool, and after that first selection round, there might be only 10 or 100 sequences that are left. At that point, we have to amplify those sequences up so that it’s a useable amount of DNA, so we use PCR (polymerase chain reaction) — which is like a photocopier for DNA — and then we start the process again. Usually after one round we’ll have a mix of okay binders and good binders and bad binders, but then we’ll do multiple rounds, maybe 12 to 20 rounds of this selection, and every time we can make the selection a little bit harder. We can change the conditions a bit, change the temperature, salt, depending on what we want to do with the aptamer in the end. Hopefully by the end we have lots of copies of a few sequences that have a good affinity and a good specificity, for whatever target we’re looking at.
That whole process is called SELEX (systematic evolution of ligands by exponential enrichment). We didn’t invent it; it’s been around since the 1990s. Depending on what you want to use the aptamer for, you can modify SELEX, because it’s an in vitro process. For the most part, if you’re trying to find an antibody, you’re using a living host: maybe a mouse, or a goat, so the antibodies are going to bind under physiological conditions. For aptamers, we do everything in a beaker, so we can control the conditions, and they don’t have to be physiological conditions if we don’t want them to be. So that allows them to be more general. Also, because they’re synthetic, there’s less batch-to-batch variability, because we can always remake the same sequence.
Maria DeRosa’s lab explains the process of SELEX through dance top
ACCN: Still, it seems like this process depends largely on luck.
M.D.: Exactly. In our lab we’ve been actually pretty lucky; we’ve had success with every kind of selection that we’ve tried, but I think in general you have a 50-50 chance that you could actually do a full selection and end up with nothing. You could mitigate that a little bit, depending on what targets you’re looking at. We know that DNA can do things like hydrogen bonds, it can do interactions through the bases, it has a negative charge on the backbone, so you can have some electrostatic interaction. You can choose your targets wisely and you’ll have more success in selection, but even then, sometimes you just don’t find anything in your pool.
ACCN: Speaking of choosing your targets wisely, what targets have you chosen?
M.D.: We want to do sensors that could be related to brain chemistry, and maybe one day [we can] study the brain directly. Dopamine is a big one that we work with; we do have an aptamer that binds dopamine, and we are now working with a neuroscience collaborator to develop sensors that will detect dopamine in mice.
Another one that we’re working on is a toxin, fumonisin B1. This toxin comes from mold, which can be present on crops like corn. Even if there’s a very, very low amount of mold these toxins can be produced, and if they are present in the corn that can make it unsafe for us to use for food. We’ve developed an aptamer now for fumonisin, and we’re trying to develop some kind of simple testing mechanism, sort of like a pregnancy test, something really easy that people at the farm or in the grain elevators could use to quickly sense if they have a problem with this toxin in their crops.
ACCN: So finding an aptamer is only the beginning, you still have to make that binding detectable in some way?
M.D.: Exactly. We have to modify the DNA in some way, and that’s another whole aspect of what’s going on in the lab. We’re doing things like modifying the DNA with probes that either change colour when there’s some kind of binding event, maybe they’ll give off fluorescence, or the fluorescence will turn off if the binding event happens. We have other kinds of collaborations where we’re modifying a fibre optic cable so that the surface of that fibre optic cable is covered with these aptamers. We can use aptamer binding to affect the property of the light, so that you can detect these things remotely.
ACCN: Are there any non-sensing applications?
M.D.: We have another target, in collaboration with Agriculture Canada. We’re interested in developing something called a smart fertilizer, which is a coating that would only release the fertilizer when the plant or the crop needs that fertilizer. It turns out that wheat and corn, when they’re in their growing cycle, release all kinds of molecules to the ground around them, and some of those molecules are essentially signals. Imagine we have this fertilizer and it has this coating on it, and inside the coating is an aptamer that binds to that signal. That aptamer-target binding disrupts the coating, so that only at that point does the fertilizer leave that particle. We’ve been working to find aptamers that will detect and recognize these signals that are coming from the crop. Then we’ve been putting them into these films and we’ve actually been able to show that these films become more permeable, so they’ll release stuff when the aptamer actually binds to the target. If you’re only going to give it to the plant when the plant says “I need it,” chances are it’s going to get used the most efficiently.
ACCN: What limiting factors need to be overcome in order to move toward commercialization?
M.D.: It is. The cells don’t feel the environment is foreign to them; they’re mechanically similar, we can engineer the chemistry to be similar, so that’s certainly a huge advantage for any type of application where the material is inside the body.
ACCN:You’ve talked about aptamers for neuroscience, food safety and agriculture. What is the makeup of your lab like?
M.D.: I try to seek out a varied background in my grad students. I have biochemists, I have chemists, I have people who are interested in nanotechnology, I have a physicist, who has now moved into chemistry, I have people that were doing computer science before, who are now doing chemistry. They do need to have a certain background, but I actually like it better if they have something a little bit different to bring to our team. I’m actually learning from my students just as much as they’re learning from me.
ACCN: On that note, can you tell us about how your team won the worldwide “Dance your Ph.D.” contest?
M.D.: It’s very funny. Science magazine has this contest to encourage people to submit
videos about the research they were doing for their PhD: If you had to explain what you were doing in your
research in a dance, what would you do? It was one student in particular, Yasir, who sent an e-mail to
everyone in the group as kind of a joke. And I loved it, because SELEX would be an amazing thing to dance.
You can imagine people coming in and out. So they picked up on it and they ran with it. I didn’t plan it, I
didn’t choreograph it, I didn’t have anything to do with it besides encouraging them, and the students did an
amazing job. I’ve been getting feedback from people around the world who are using this to teach what SELEX
is all about. It was informative, it was actually accurate, in the sense of the steps that we have to go
through, and it was entertaining. My mother says now she finally understands what I do, and who could ask for
something better than that? 
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