Strand transfer occurs in retroviruses by a pause-initiated two-step mechanism.

Recombination promotes retrovirus evolution. It involves transferring a growing DNA primer from one genomic RNA template in the virus to the other. Strand transfer results in vitro suggested that pausing of the reverse transcriptase during synthesis allows enhanced RNase H cleavage of the initial, or donor, RNA template that facilitates primer interaction with the acceptor template. Hairpins are common structures in retrovirus RNAs that induce pausing. Analyzing primer transfers in hairpins by base substitution markers showed transfer sites well beyond the site of pausing. We developed methods to distinguish the initial site of primer-acceptor template interaction from the site of primer terminus transfer. The strand transfer mechanism was confirmed to involve two steps. In the first, the acceptor template invades the primer-donor complex. However, the primer terminus continues elongation on the donor RNA. The interacting primer and acceptor strands then propagate by branch migration to catch the advancing primer terminus. Some distance downstream of the invasion site the primer terminus transfers, marking the genetic shift from donor to acceptor. Nucleocapsid protein (NC) is known to influence primer elongation and strand exchange. The presence of NC increased the efficiency of transfers but did not appear to alter the fundamental transfer mechanism.