Paegel's team wanted to see if they could evolve a better ligase by natural selection.The team has its sights set higher, on entirely new chemicals, saying, "We took a potato and made a really tasty potato, but we would really like to discover broccoli – something completely different." In the closed environment of a Darwin chip, that might be more difficult than in the wild and woolly world, where selection pressures can shift in catastrophic fashion, viruses can inject DNA bits into genomes, or organisms can swallow others up in symbiotic relationships.
To do this, they took a form of ligase that is not very good at recognising RNA molecules, and dumped it in a pool of RNA. After letting it duplicate for a while, the researchers gradually reduced the number of RNA molecules in the pool, meaning that only the more efficient copies of the ligase could survive.
All the reactions occurred in a miniature chamber on the "evolution chip". After reaching a specified level of efficiency, a miniature pump automatically sucked up a small amount of the contents and plopped it into a new chamber. This started another round of selection.
After 70 hours and billions of duplications, Paegel's team stopped the reaction and analysed the last few batches. The ligase molecules they pulled out were able to find and stitch RNA molecules 90 times more efficiently than the ligase the team started with.
Apr 8, 2008
evolving RNA in real time with a "Darwin chip"
Ewen Callaway of New Scientist describes a nifty new process: