Design and analysis of a structural RNA that acts as a template for peptide ligation.

An artificial RNA, which acts as a specific template for peptide ligation, was designed and constructed. Into the P4-P6 domain of the Tetrahymena intron RNA, two peptide binding motifs (boxB and RRE) were installed. Two peptides (N and Rev) were expected to bind to the RNA simultaneously, facilitating their ligation by an entropic effect. The peptide ligation actually proceeded effectively in the presence of the designer RNA. Analysis using mutant peptides or mutant RNAs demonstrated that the peptide ligation proceeded by forming a specific trimolecular RNP complex.