Ribozymes That Benefit from Peptide Cofactors with Aromatic Modifications

The origin of life went through a stage that was driven by catalytic RNAs (ribozymes). This stage likely took place in a complex mixture with many types of molecules, including peptides. A previous in vitro selection experiment in the presence of octapeptides identified a ribozyme (Rz20) that showed a ~900-fold increase in activity in the presence of a peptide—but only if the peptide carried an N-terminal modification such as Fmoc, fluorene, or naphthalene. Here, we expand the range of N-terminal modifications to nine and include three additional ribozymes from this selection that show a more modest benefit from these modified peptides. All ribozymes showed increased activity with the Fmoc modification (used during the selection) and a fluorene modification that is chemically very similar to Fmoc. Naphthalene benefitted only two ribozymes, and the phenyl modification gave no significant benefit for any of the four ribozymes. When the five nucleobases (A,G,C,T,U) were tested as modifications, each ribozyme gave a characteristic pattern that suggested different binding modes and perhaps different functions of these peptide conjugates for ribozyme activity. Together, these data expand the number of ribozymes that use aromatically modified peptide cofactors to four and help paint a picture of how RNA could have utilized chemically modified peptides during early life stages.