Effect of the Murine Leukemia Virus Extended Packaging Signal on the Rates and Locations of Retroviral Recombination

Reverse transcriptase (RT) switches templates frequently during DNA synthesis; the acceptor template can be the same RNA (intramolecular) or the copackaged RNA (intermolecular). Previous results indicated that intramolecular template switching occurred far more frequently than intermolecular template switching. We hypothesized that intermolecular template-switching events (recombination) occurred at a lower efficiency be-cause the copackaged RNA was not accessible to the RT. To test our hypothesis, the murine leukemia virus (MLV) extended packaging signal (C1) containing a dimer linkage structure (DLS) was relocated from the 5* untranslated region (UTR) to between selectable markers, allowing the two viral RNAs to interact closely in this region. It was found that the overall maximum recombination rates of vectors with C1 in the 5 * UTR or C1 between selectable markers were not drastically different. However, vectors with C1 located between selectable markers reached a plateau of recombination rate at a shorter distance. This suggested a limited enhancement of recombination by C1. The locations of the recombination events were also examined by usin