A design principle for a single-stranded RNA genome that replicates with less double-strand formation

Usui, Kimihito; Ichihashi, Norikazu; Yomo, Tetsuya

In the above-mentioned experiments, we used Q␤ replicase that contained a host factor, the ribosomal S1 subunit. To investigate whether the dsRNA ratio observed was dependent on the host factor S1, we performed RNA replication using core Q␤ replicase lacking the S1 subunit, both in the presence and the absence of the S1 subunit. We used three RNA templates (MDV-1, 4. Loop GA10, and 22. Stem GAmis8) with varying GC numbers in the inserted Figure 3 , and the total RNA synthesis (A) and dsRNA ratios (B) were measured. The inserted sequences were designed to form two different stable structures (a large stem or two small stems). The probability of forming the two small stems was designed to increase as the RNA number (23-28) increased. Error bars indicate the standard deviations (n = 3). loop (3, 6 and 12, respectively). Presence of the S1 subunit decreased the dsRNA ratio for all three RNA templates, consistent with a previous report (8, 23) . However, the tendency of increasing dsRNA ratios, dependent on the GC number in the inserted loops, remained unchanged even in the absence of the S1 subunit (Supplementary Figure S5) . This result indicates that the relationship between the dsRNA ratio and the GC number in loops is independent of the presence of the S1 subunit.