Development of a functionally minimized mutant of the R3C ligase ribozyme offers insight into the plausibility of the RNA world hypothesis

Abstract

The R3C ligase ribozyme is an artificial ligase ribozyme produced by modification of the ribozyme that lacks cytidine. Here, we attempted to modify the original R3C ribozyme (73 nucleotides) by reducing the number of nucleotides while maintaining the maximum possible catalytic efficiency. By partially deleting both the "grip" (P4+P5) and "hammer" (P3) stem-loops, we found the critical border to retain activity comparable to that of full-length R3C. The three-way junction structure was necessary to maintain enzymatic function and the stability of the "grip" (P4+P5) stem had a large influence on the catalytic activity of R3C. The final minimized ribozyme we obtained comprised~50 nucleotides, comparable to the estimated length of prebiotically synthesized RNA. Our findings suggest that the autocatalytic function in ribozymes is indeed possible to obtain using sequence lengths achievable with prebiotic synthesis. © 2014 by the authors; licensee MDPI, Basel, Switzerland.