Quest for self-replicating RNA edges closer to life’s possible origin

RNA can’t copy itself, but can copy over 200 bases of other RNAs.

John Timmer – Oct 25, 2013 11:30 am | 17

The discovery of nucleic acid molecules that can catalyze chemical reactions has revolutionized thinking about the origin of life. These catalytic RNAs, called ribozymes, showed that a single molecule could embody two of the major aspects of life: genetic information and chemical activity. They also raised the intriguing possibility that it might be possible to find an RNA molecule that could copy itself. After all, once you have a single self-duplicating molecule, you would quickly end up with a large collection of self-duplicating molecules competing for resources. Evolution would be off and running.

So far, though, efforts to make a self-replicating ribozyme have come up short. Most RNA molecules with this sort of activity have been around 200 bases long and have tended to stall before copying more than a few dozen bases. But now, scientists have produced the first molecule that can copy RNAs longer than itself. The scientists found it by selecting for RNAs that work in conditions that are normally the death of biochemical activity: sub-zero mixtures of ice and water.

Makin’ copies

The path to a potential self-replicating RNA has, so far at least, been a bit convoluted. Starting with a collection of RNA molecules with random sequences, researchers come up with a ribozyme that could link two RNAs together (termed a ligase). Rounds of mutation meant to improve that activity succeeded in doing so, but they also popped out a different class of molecules entirely; they could make copies of a specific group of short sequences. Further experiments with mutation and selection made these catalytic RNAs work more generally and extended the molecules they could copy to longer sequences. But the RNAs themselves were over 200 bases long, and they tended to fall short of copying molecules that were much smaller than that.

The Cambridge researchers behind the new paper noticed something unusual. Although this catalytic RNA was originally evolved to work at room temperature, it worked even better on ice. Ice tends to slow down reactions, but partly freezing a solution will cause the remaining salts and RNA to concentrate in the gaps between the frozen ice. A network of water-filled crevices tends to form, and the water within them stays liquid to well below 0°C, giving the ribozymes something to work with. (Environments like this currently exist in polar regions.)

If the ribozyme worked well on ice as-is, the authors reasoned that it would work even better with a chance to adapt to the cold environment. So they subjected the ribozyme to a few rounds of mutation, followed by selection for its ability to copy RNA molecules in an icy environment. The RNA they produced this way not only worked better in the cold environment, but it was more active in all conditions tested, including in temperatures up to 27°C.

That increased activity produced the ability to copy longer RNA molecules for the first time. In fact, the paper’s authors were able to get their ribozyme to copy one that was 206 bases long, while the RNA that did the copying was only 202 bases long.

It’s great progress, but the result still comes far short of a molecule that can copy itself. For one thing, the ribozyme tended to stop short of the end of the molecule it was copying, mostly because the two fell out of contact. The authors could tether the two RNA molecules (the ribozyme and the template it was copying) together, which improved matters but didn’t solve the problem entirely. The second problem was the fact that the molecule being copied folded over and formed base pairs with itself, which prevented the ribozyme from copying through the folded structure.

This creates a serious problem since the activity of the ribozyme depends on it being able to fold into a three-dimensional structure—which creates a bit of a chicken-and-egg problem for making a self-replicating ribozyme.

The authors suggest that the way around this issue might be to make the molecule even longer. If they could find a ribozyme that disrupts these folds, it might be possible to link it to the one that does the copying. Combined, the two may be able to work their way through copies of even large molecules. Ultimately, this could be the route to building the first self-copying genetic molecule.

Nature Chemistry, 2013. DOI: 10.1038/NCHEM.1781 (About DOIs).