Targeting the site of RNA-RNA recombination in brome mosaic virus with antisense sequences

It has been postulated that local hybridizations between viral RNAs can mediate recombination in brome mosaic virus (BMV) and in polio virus. To test this model, a 3′ fragment of BMV RNA1 was inserted into the 3′ noncoding sequence of BMV RNA3 in an antisense orientation. This resulted in high-frequency nonhomologous crossovers at or near the hybridized region. Insertion of the same RNA1 fragment in a positive-sense orientation did not promote recombination. Modification of the antisense insert by deletion of 3′ portions did not affect the sites of crossover. However, modification of the 5′ portion shifted the crossovers toward the central part of the heteroduplex region. Our results provide experimental evidence that recombinant crosses can be primed by hybridization between viral RNA molecules.