Engineering Autonomously Folding RNA Scaffolds from the Large Ribosomal Subunit

Increasingly supportive studies of the RNA World hypothesis have revealed that the self-recognition and catalytic properties of RNA may have provided the foothold needed for early life to have arisen from abiotic chemistry. Previous demonstrations of in vitro selection and evolution experiments have produced artificial RNA ribozymes from random pools of RNA sequences capable of supporting an RNA-mediated metabolism, including the chemistry needed for RNA replication, but observe limited catalytic activity and fidelity. The discovery of increasingly sophisticated ribozyme activities has been limited by the effective sampling of RNA sequence space from synthetic RNA pools, generally restricting RNA architectures to structures of 200 nucleotides (nt). Through the rational design and characterization of a series of large (~400 nt) ribosomal domain-III scaffolds, inspired by the autonomously folding Thermus thermophilus ribosomal domain-III, we lay the foundation for a scaffold lineage designed for eliciting novel ribozyme chemistry and improved efficiency through in vitro selection and evolution