Importance of Metastable RNA Folding in Template‐Replicase Interactions

Abstract

We consider the autocatalytic synthesis of MDV-1 RNA by Q beta replicase, which proceeds by template-instructed replication. We predict the effect of a particular point mutation in the sequence on the overall doubling time and conjecture its role on the recognition step. The mutation considered destabilizes the folding of the internal recognition site. The theoretical analysis is based on the calculation of nonequilibrium re-folding events which occur in the RNA chains as they are being synthesized. Free-energy minima are irrelevant. In order to test the theoretical findings, we incubate both the natural template and the mutant simultaneously, in the presence of the replicase. The experiment reveals that the mutation facilitates the enzyme-template interaction, thus enhancing recognition. However, examining the exponential phase of the replication kinetics, where the enzyme is in large excess with respect to the RNA species, we can conclude that the mutant presents a larger overall doubling time, in good agreement with our theoretical findings.