A PREFERRED TARGET DNA-STRUCTURE FOR RETROVIRAL INTEGRASE IN-VITRO

The retroviral integrase protein catalyzes the insertion of linear vir al DNA ends into the host cell DNA. Although integration in vivo is no t site-specific, the detection of local and regional preferences withi n cellular DNA suggests that the integration reaction can be influence d by specific features of host DNA or chromatin. Here we describe high ly preferred in vivo integration sites for avian sarcoma virus and hum an immunodeficiency virus-1 integrases within the stems of plasmid DNA cruciform structures, The preferred sites are adjacent to the loops i re the cruciform and are strand-specific. We suggest that the observed preference is due to the end-like character of the stem loop structur e that allows DNA unpairing. From these results we propose that such u npairing may enhance both the processing and the joining steps in the integration reaction, and perhaps other cellular recombination reactio ns as men.