Using 'molecular scissors' to snip COVID

How artificial enzymes can be programmed to attack COVID
25 November 2022

Interview with 

Alex Taylor, CITIID


Green coronavirus particles around a strand of DNA.


Precision molecular scissors that can operate inside our cells to selectively target and dismantle the genetic material of the COVID-19 virus have been developed by researchers at the University of Cambridge. Dubbed XNAzymes, the scissors are themselves built from short pieces of an artificial genetic material called XNA. This folds itself into specific shapes that can recognise and target for cutting only the genetic sequences of  viruses, rather than any of the healthy genetic material that's meant to be in a cell. And by building sets of these molecular scissors that are effectively multi-bladed, they can be programmed to make cuts in the viral genetic material at several locations; so even if the virus adapts or mutates in one of the cut sites, it will still be disabled by cuts made elsewhere. Alex Taylor, from the Cambridge Institute of Therapeutic Immunology & Infectious Disease, CITIID, is here to explain how they've done this...

Alex - If you imagine the double helix like you sort of get with a short piece of DNA, sort of peeled apart into its two separate strands, one of those strands by itself can fold up into really a variety of different shapes. But in our case, the strings of nucleotides are made from these artificial building blocks. That's what makes them XNAzymes. They're strings of just sort of 35 or so of these. So that makes them about sort of 10 nanometers long. Just to sort of put that in context, it means you could sort of fit about five to ten thousand of these things across the width of a human hair. We know what the sequence of XNA that you need to sort of fold up into an active enzyme, but we actually don't know yet what the sort of catalytic core of these things looks like. But we know they have a sort of catalytic core with a kind of couple of binding arm sequences next to these that recognize the RNA. And in the study, as you say, we sort of took three of these XNAzymes, these molecular scissors and engineered them to sort of fold up into kind of pyramid like structures. So a bit more like a sort of three bladed blender.

James - How do you get them physically into the cells for them to then do their work?

Alex - Well, so for us it's very early days. We are just trying to understand whether and establish whether these things can actually have their kind of catalytic activity inside cells. So at the moment we've just been using this technique called electroporation. So this is where we give cells a little electric shock and that sort of opens up temporary sort of holes in the surface of the cell and allows the XNAzymes in. This isn't really a technique that we could use in a sort of realistic clinical setting. So in the future we want to explore sort of linking XNAzymes to things like the sort of fatty droplets as this is the kind of technology that was used for tthe Pfizer and Moderna RNA vaccines. But actually other researchers have shown that in the case of things like lung cells, it might be possible to sort of just inhale short oligos into the lungs in a fine mist and get them taken up into cells without having to rely on things like lipid nanoparticles.

James - And how effective have they proven to be in what you're trying to achieve with them?

Alex - So far we started off by sort of just in the test tube taking sort of short sections of the viral genome of SARS-2 and sort of linking these to kind of glowing dyes that allows us to kind of track the size of these RNA target molecules. And it was part of the exciting aspect of this technology is that we could rapidly generate a series of the XNAzymes really just within a couple of days of the genome coming out and sort of test whether they worked on these shorter fragments. And once we'd done that, we moved over to using the full RNA genome of the virus extracted from infected cells, tested them sort of with conditions that kind of mimic the inside of the cell. And again, once we saw that it was cutting, I was able to team up with a virology lab in my department who have a sort of safety level three lab and we challenge cells with a live virus. And we found that indeed once the cells have XNAzymes in them, they're able to inhibit the replication of the virus.

James - And just finally, Alex, could this technology be used for other diseases or recurrent infections?

Alex - Absolutely. So at the moment we're really only targeting RNA based viruses. But this includes some of the biggest kinds of emerging threats that we face over the last few decades. So things like Ebola, Zika, influenza, this kind of thing. So we certainly think that we should be able to know we're looking at sort of targeting some of these kinds of viruses. And really RNA viruses are really the big sort of scary group. About 40, 40 to 50% of emerging human infectious diseases are RNA based viruses. So, at the moment that's, that's where we're sort of putting our attention.


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