16 The Shapely mRNA: Knotting Ventured, Knotting Gained

Abstract

Replicate, replicate, replicate! That is all that counts for a fledgling, evolving RNA molecule bent on survival. Alternative RNA sequences that improve the replication rate will compete better in the soup and live to see another day. And evolution of any additional functions will be measured by their effect on the replication facility, including rate and, more subtly perhaps, the crucial balance between accuracy and limited sloppiness of replication.

The primitive encoding of an amino acid sequence would only have been preserved and enhanced through evolution if the peptide product helped replication. Presumably, in this sparse environment, the product would have to act directly on the molecule that produced it. If an encoded peptide product were released from the replicating molecule, it would diffuse away and be of no evolutionary use. (Appropriate surfaces might help keep encoded molecules nearby, but the geometry would be demanding. Or, a primitive membrane might contain the molecules, although diffusion of precursor molecules into the enclosed space presents a real problem.) How might a primitive peptide help replication, even a little, which is all that is necessary? The easiest peptide to make by an evolving encoding mechanism would likely be a polyamino acid such as glycine or alanine, the amino acids thought to be the most primitive (Trifonov 2004; see also Jordan et al. 2005; Yarus et al. 2005). Although these amino acid sequences might be simple, a peptide such as polylysine could help replication by neutralizing charge on the RNA and lowering the energy...