Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications

In addition to completing the Watson Crick nucleobase matching concept (big pairs with small, hydrogen bond donors pair with hydrogen bond acceptors), artificially expanded genetic information systems (AEGIS) also challenge DNA polymerases with a complete set of mismatches, including wobble mismatches. Here, we explore wobble mismatches with AEGIS with DNA polymerase 1 from Escherichia coli. Remarkably, we find that the polymerase tolerates an AEGIS:standard wobble that has the same geometry as the G:T wobble that polymerases have evolved to exclude but excludes a wobble geometry that polymerases, have never encountered in natural history. These results suggest certain limits to structural analogy and evolutionary guidance as tools to help synthetic biologists expand DNA alphabets.