In this thesis, applications of aminoacylation ribozymes named
flexizymes are described. Flexizymes have the following unique
characteristics: (i) substrate RNA is recognized by two
consecutive base pairs between the 3'-end of substrate RNA and
the 3'-end of the flexizyme; (ii) these base pairs can be
substituted with other base pairs; and (iii) various activated
amino acids can be used as substrates including both canonical
and noncanonical amino acids. This flexible aminoacylation of
RNAs by flexizymes was used to label endogenous tRNAs to be
removed, and in vitro selection using the tRNA-depleted library
enabled the discovery of the novel interaction between the
microRNA precursor and metabolites. Flexizymes are also used to
prepare various aminoacyl-tRNAs bearing mutations at the 3'-end
to engineer the translation machinery and to develop the
orthogonal translation machinery.
The first part of the research demonstrated that SELEX is appropriate for discovering the interaction between small RNA and ligands, and suggested that more RNA motif binding to small molecules exists in small RNAs. The second part opened a door to new opportunities for in vitro synthetic biology involving the engineering of the genetic codes and translation machineries. This research also indicated the great potential of aminoacylation by flexizymes to be applied in various fields of RNA research, which is beneficial for RNA researchers.