Secondary structure of RNA from bacteriophages f2 Qbeta, and PP7

Electron microscopy of RNA-protein monolayers prepared under partial denaturing conditions has been used to compare the secondary structure of coliphage f2 and Qbeta and Pseudomonas aeruginosa phage PP7 RNAs. The secondary structure map of f2 RNA contains a central open loop and four symmetrically placed hairpins, which is similar to the pattern reported by Jacobson (A. B. Jacobson, Proc. Natl. Acad. Sci. U.S.A. 73:307-311, 1976) for the closely related phage MS2. With the same denaturing conditions, Qbeta RNA, which is 20% larger than f2 or PP7 RNA, has a central open loop and a smaller terminal loop. PP7 RNA has two large, closed secondary structures, one of which is nearly central. The base composition of PP7 RNA was determined and is similar to that of the group I coliphage RNAs. Thus, the greater amount of large base-paired structure is not related to an increased guanine-plus-cytosine content of PP7 RNA. With increased denaturing conditions, the central, closed structure of PP7 RNA is converted into an open loop. The central structures of all three phages include about 700 nucleotides. The relevance of these findings to the genetic maps of the coliphage RNAs is discussed.