Science Friday - Scientists Create Glowing ‘RNA Lanterns’ With Bioluminescence

Episode Date: February 6, 2025

The inner workings of our bodies, particularly what’s happening inside our cells, can be kind of a black box—with countless tiny molecules constantly working and churning to keep us alive. A new technology that blends bioluminescence with cellular machinery may shine some light on the details of their comings and goings and interactions that can be hazy.Scientists had the bright idea to take that same enzyme that makes fireflies glow and tie it to RNA, the molecule that reads the genetic information in DNA. This developing technology has been used on mice, with the hope that these light-up molecules can help illuminate how viruses replicate or even how memories form in the brain.Flora Litchtman talks with Dr. Andrej Lupták, professor of pharmaceutical sciences at the University of California Irvine and Dr. Jennifer Prescher, professor of chemistry at the University of California Irvine, about their research on the topic.Transcripts for each segment will be available after the show airs on sciencefriday.com. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

This is Science Friday. I'm Flora Lichten. Today in the podcast, scientists have figured out how to attach a tiny lantern to a key piece of cellular machinery. We're very much interested in being able to use the lantern to be able to track the spread of different viruses to learn more about ways to treat infection. The inner workings of our bodies and our cells can be kind of a black box. We know that all these itsy-bitsy molecules are constantly working and churning to keep us alive. But the details of their comings and goings and interactions can be hazy. But a new technology that blends bioluminescence with cellular machinery may shine some light. Scientists had this bright idea.

Take that same enzyme that makes fireflies glow and tie it to RNA, the molecule that reads the genetic info, DNA. And the hope is that these light up molecules can help illuminate how viruses replicate or even how memories form in the brain. Joining me now to tell us more about their research are my guests, Dr. Andre Louptock, Professor of Pharmaceutical Sciences at the University of California, Irvine, and Dr. Jen Pressure, Professor of Chemistry at the University of California, Irvine. Welcome to Science Friday. Hello. Great to be here. Okay, Andre, refresh our memories. Remind us quickly what RNA does? Well, RNA is the first molecule that gets made as the genetic information that's

encoded in DNA is executed. And the first thing that would happen if you say, okay, go do this, go do that. That, on the molecular level, what you're doing is you're expressing an RNA, you're making an RNA molecule. So it's the first act of gene expression. So I think of RNA kind of like the middle manager, like it takes direction from the DNA and then it delegates, right, to the cellular machinery that will make it happen. Is that the right analogy? Yeah, yeah. That's a really good way to think about it. But it has its own functions in its own right. Sometimes it catalyzes chemical transformation. Sometimes it acts in regulating other cellular processes. So you attached this little lantern to it. Is that the right way to think?

think about it, Jen? That's absolutely right. We took a well-known light-emitting system in nature, these bioluminescent probes, which comes from a luciferase reaction with a luciferin small molecule, and that creates light. And we use those components and drag them to RNAs of interest. And so when the RNA was produced, we had the light-emitting enzyme dragged. to it and then we could see light production relevant to the presence of the RNA itself. How long does that little firefly lantern stay on? Like, is it on indefinitely? In the first system that we produced, we designed the lantern to stay on for the lifetime of the RNA. So whenever the RNA was present, the light would be there. And whenever it wasn't, we would see

no light. How do you know that the lantern isn't messing up the function? of the RNA. It isn't sort of like getting in the way or mucking up what the what the RNA does. The key aspect of our work was to design and then optimize a tiny, tiny, tiny RNA that is a module. And we spend a good two years making sure that it's independent of other parts of other RNA. So it's basically a little, like a little solid rock that the luciferase binds. We don't have any evidence that that part of the RNA interferes with any other function of the, of a longer RNA that it may be part of or another RNA in the cell. So you popped it on a place on the RNA that's not doing anything else?

That's right. Okay. And so why RNA? Like, why illuminate its comings and goings? The scientists have been illuminating many aspects of the cell for many years. For RNAs is a couple of decades behind what other areas of particularly protein, studying proteins that has been doing. And so it was simply a gap that we wanted to fill because we had questions about where

RNA was produced, when it was produced, and where it was going. And we wanted to understand this on levels from basically single molecule all the way to a living mouse. What does this look like? What's the readout of this? Can you help me picture it in my mind? The light emission that we're using here isn't bright enough to see with your own eyes at this level, but we use really sensitive cameras, similar to those that are used by astronomers and so forth

to collect every last little photon coming out of a given system. And those then create a snapshot of the lantern and the associated RNA at a given time. Are you saying that we're using sort of like telescope technology to look inside the body? Absolutely. There's different ways of thinking about how to observe things. And the telescope analogy here is a good one because we're trying to put the largest lens we can over our experiment and then essentially tie it to a very, very sensitive camera. What are the questions you're excited to investigate with this new technology?

Oh, my. That's another part of our every week, something else comes up. We would like to know when, in a live mouse, when a memory forming event takes place and then RNA is expressed that is related to that memory formation. Wait, you're going to have to back up. A memory forming event? Well, it's something that a mouse would remember. How is RNA related to that? I think we think of neurons and synapses, but tell me how RNA plays a role or might play a role. Well, in all events that are meant to leave a lasting effect, so that would be a memory, RNA is involved because you, in a neuron, an RNA is made to then code for a protein that is

involved in, for example, a strengthening of a synapse. So ultimately, the synapse may be built out of membrane and membrane proteins, but the information that codes for it is delivered locally via an RNA. Neurons are particularly interesting because they're large. They're huge cells. It's a long way from a nucleus to a synapse in certain neurons. And so there is a lot of questions related to transport levels of expression. How does it find its way?

When does it go there? We have answers to these questions from cell culture experiments that has been done over the past almost about three decades. But in a live organism, we have not seen that. We would really love to. It sounds like RNA are sort of making the tiniest building blocks of memories. And this technology would allow you to sort of see those blocks being placed. Is that a sound about right? Yeah, that's a good way of thinking about it. We think of it more of how the information is moved from the nucleus where the DNA is stored. And, you know, you've parked your car today. you want to find your car when you come back.

So could this technology be used to help us make better mRNA vaccines, for example? We believe so. We think any time you have a tool, a molecular tool that lets you visualize something fundamental, a key technology where you know where you're putting it, at what point does it enter the cell, you know, how quickly does it enter the cell? And ideally which cells are affected? You know, we can then use that as a tool to build better vaccines and deliver the MRNAs to places more precisely, for example. What about viruses? I mean, they're made of RNA often, right?

Could you add your lantern to a virus? Absolutely. The lanterns can report on RNAs from not just human cells, but also those from different viruses. and we're very much interested in being able to use the lanterns and different colors of lanterns to be able to track the spread of different viruses and models to learn more about the underlying biology and potentially then ways to treat infection. We have to take a break, and when we come back, why it took over a decade to get this technology off the ground?

I think people didn't think it would work. Well, we know that because we got the reverse. views. They told you. So that would be revolutionary, right? Being able to watch a virus move through the body. Right. Being able to watch the spread of viral infection over the whole organism would provide some novel insights into the spread of infectious disease and things that we might not even realize are happening. And that then leads to better avenues for treatment. How long did it take to get this to work? Why are you laughing?

This project was sort of years in the making. Andre and I have been colleagues at UC Irvine for almost 15 years now, and these have been sort of ideas that have been percolating, I think, over the entire 15-year period. And within the past five years or so, we really started to focus on this aspect of using luciferases to tag RNAs. Andre is an expert in RNA biology, and I have done a lot with developing luminescence technologies over the years, and so that was sort of a natural fit. But there was so many things that needed to be optimized to pull off these types of experiments, from designing the RNAs to designing the lantern proteins, to developing the small molecules and the instrumentation and analyzing cells and whole organisms.

So we really needed a whole kind of dream team of people also to come together, including one of our close collaborators on this project, Oz Stewart from the Neuro Biology Department here at UC Irvine. And then we also had a really outstanding team of students that got this project off the ground. And I think without them, we couldn't have spanned this highly interdisciplinary area to pull this off. What do you think, Andre? I agree. And one other thing was about nine, 20 years ago, we started writing proposals to get this funded, to get it going. And it was a struggle for a while.

You know, it took time to both assemble the team and find the support for it. Well, I want to ask about that. It was a struggle because it was basic research or because people didn't see the value or people didn't think it was going to work. What was the struggle? I think people didn't think it would work. Well, we know that because we got the reviews. They told you. You know, early on, some of the reviews we got were, well, you guys will never have enough photons to see what you think you will see.

You know, it's challenging to convince others that are used to looking at a much stronger signal that we will see what we think we will see. and it'll be in real time with good spatial resolution. And ultimately, that's what ended up happening. But it took a while. What did it feel like when it did start working? Oh, it was amazing. It was awesome. Yeah.

You know, in some ways we got, I wouldn't say lucky, but we had a hint that it was going to work right when we finally had the team assembled. When we started working on this in earnest, we had a smidget of a signal that we called it the 1.2 day. Yes. And it was the signal that the signal of our background was 1.2. So you can imagine it wasn't much. That's a very scientist way of saying like very little was coming through, right? Very little was coming through.

And, you know, we were reasonably convinced that, yes, that signal is real. And so let's just work on it. Let's optimize. let's engineer this, let's hit it from every angle. And, you know, that 1.2 turned into about 4,500, ultimately. The effort led to about 100-fold improvement. Yeah, I would definitely say that every week, it seems like there's some exciting eureka moment with the images and things that we've been generating.

And this group gets together every Friday to go over the latest. and I think that feeling of excitement that came from the 1.2 fold measurement early on, that has sustained itself through all of these weekly meetings over the years. Are people knocking down your door to get a hold of this, other scientists? We certainly had people reach out to acquire the different sequences and the different lantern components that we've been using. One of the most fun things about being involved in imaging tool and technology, lead you development is to see just how far and wide it is applied and the new insights it can

bring beyond the applications that we're performing in our own lab. What's next for you two? More photons. Well, you know, we're very, very excited about this. And some of the experiments that we described, you know, including with RNA viruses, with MRNA delivery, and in particular in neurobiology, in neurons. Those are the key areas that we're working on. When do you think we're going to start seeing sort of new discoveries using this tech?

Like when will we, when do you expect we might learn more about how memories are formed or start tracing viruses in the body? Well, I think the viral work can be quite quick. it's really just putting these tools into the viral DNA and then doing fairly standard virology experiments. So, you know, it depends on how well it works. But that should be months. The questions related to neurobiology tend to be slower. I think we're looking at some couple of years. The brain's a complicated place. Sure. Yes, indeed. Thank you so much for joining us today. Thanks for having us. Our pleasure. Thank you.

Dr. Andre Louptock, Professor of Pharmaceutical Sciences at the University of California Irvine, and Dr. Jen Pressure, Professor of Chemistry at the University of California Irvine. Before we go, last week on the show, we talked about the winter doldrums and how to do winter better. And you all had a lot to say. We got calls from around the country. My name is South Parkovson. I live in Jackson Hole, Wyoming. This is Ali from Hawaii. Hi, this is Daniel from Chicago.

You winter lovers were out in force with your tips and tricks and some perspective shifts for how to get through the coldest, darkest days. My favorite day of the year is December 22nd because that is the day that the days start getting lighter and lighter every single day. So that's my biggest celebration day and that helps me. You don't really need coping mechanisms for the winter. You just go cross-country skiing every day. That's what I do. Also being a surfer and the winter being the season when the surf comes, we look forward to winter every year.

Hi, Science Friday. I live in Norway and it's so dark here and it's so cold. I have a lamp, quite a large lamp that I have on a time clock and that comes on and that totally lights up the whole bedroom like so much. and it's a bit of a shock, but I can hide myself under the duvet for a bit, but then after a short time, I'm wide awake. And this is my survival in the winter time. We also floated this idea of rebranding winter. You know, like forget the winter dull drums, the winter blues.

Instead, we need a pro-winter catchphrase. And I wanted to share one of my favorite submissions. Well, it seems January jollies and February follies, no doubt. No doubt. This is Christopher Parks. I'm from Somerset, New Jersey. Thanks, Christopher, and to everyone who called. And if you have a message for us or a question about winter things or any other things, give us a call. Our number is 646-76-767-6532.

646-6-6-6-6-6-3-2. We always want to hear from you. You can also email us at SciFri at ScienceFriD.com. And that is about all we have time for. Lots of folks helped make the show happen. including George Harper, John Denkowski, Annie Niro, Jason Rosenberg. I'm Flora Lichten. Thanks for listening.