Preferred sites of recombination in poliovirus RNA: an analysis of 40 intertypic cross-over sequences

The genome of poliovirus consists of a single strand of RNA approximately 7.5 kb long. Analysis of the sequences around 40 unique recombination sites reveals several features that differ significantly from those expected of randomly located sites. These features, which include a broad zone of elevated homology on the 3' side of the cross-over, support the theory that RNA recombination occurs by a template-switching mechanism during synthesis of the complementary strand, and that sites are chosen to minimise the adverse free energy change involved in switching to a heterotypic template. There is also a strong sequence bias, almost two-thirds of cross-overs, according to a computer simulation, occurring immediately after synthesis of UU. These features shed new light on the extent of base-pairing in replicative intermediate RNA, and on the mechanism of chain initiation.