RNA secondary structures of the bacteriophage φ6 packaging regions

Abstract

Bacteriophage φ6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only φ6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for φ6, and the packaging signals (pac sites) have been mapped to the 5′ ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of φ6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.