Alternative homologous and nonhomologous products arising from intramolecular recombination.

RmI, a chimeric DNA molecule containing polyomavirus (Py) and mouse sequences, generates unit-length Py DNA via intramolecular recombination between two directly repeated viral sequences of 182 base pairs (S repeats). To analyze the contribution of the S repeats in this process, we produced mutants of RmI carrying deletions in either one or both S repeats and tested them for their ability to recombine in mouse 3T6 cells. Mutant DNAs were found to yield unit-length Py DNA as long as they carried a minimal internal homology of 40 to 50 base pairs. Unlike RmI itself, however, the mutants also gave rise to nonhomologous recombination products. These results suggest that when the generation of homologous products is hampered by a limiting homology, nonhomologous products may arise instead of homologous ones. Therefore, the initial step(s) in the mechanisms yielding the two kinds of products could be identical.