Pause sites and regulatory role of secondary structure in RNA replication

We analyze the correlation between pause sites and changes in enzyme boundaries within the elongation complex in template-instructed MDV-1 RNA replication. A Monte-Carlo simulation is carried out to follow the refolding events in the replica and in the portion of template strand upstream of the site where nucleotide incorporation takes place. We introduce and verify the hypothesis that the refolding events upstream of the replication fork are involved in the regulation of replication by leading to a partial relaxation of interaction between the enzyme and the growing chain. This relaxation is carried out by replacing enzyme-product binding by intra-chain pairing of the bases involved.