Kinetic model of double-stranded RNA formation during long RNA replication by Qβ replicase

Qβ replicase is an RNA-dependent RNA polymerase, which synthesizes the complementary RNA using a single-stranded RNA as a template. The formation of non-replicable double-stranded RNA (dsRNA) by hybridization between newly synthesized RNA and the template RNA hinders the broader application of Qβ replicase. Here, we developed a kinetic model of Qβ RNA replication consisting of two reaction pathways of dsRNA formation, which quantitatively explains the dynamics of dsRNA formation of three template RNAs. We also found that part of the Qβ phage genomic RNA sequence including the central hairpin loop significantly decreases the rate of dsRNA formation.