Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination

Recombination between RNAs associated with turnip crinkle virus is1Department of Biochemistry and Molecular Biology thought to occur during plus-strand synthesis at motifs resembling the Program in Molecular and 5'-ends of genomic, subgenomic and satellite RNAs. Common structural regions encompassing the motifs have been found for major crossover sitesCellular Biology and on two different minus-strand templates, with junctions preferentially2Department of Microbiology located in a single-stranded region at the 3 ' base of a hairpin. Base changes, University of Massachusetts deletions and compensatory alteration constructed in and around the hairpin Amherst, MA 01003, U.S.A. in the region of the turnip crinkle virus genomic RNA involved in recombination support the importance of the hairpin for normal crossover site selection. This region of the genomic RNA is also important for replication of the viral genomic RNA in plants and protoplasts, suggesting a common link between sequences required for recombination and viral replication