HOST SITE SELECTION FOR CONCERTED INTEGRATION BY HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 VIRIONS IN-VITRO

Host site selection for full-site integration by human immunodeficienc y virus type-1 (HIV-1) integrase (IN) from nonionic detergent-lysed vi rions was investigated. Linear retrovirus-like DNA (469 bp) possessing 3' OH recessed long terminal repeal termini was efficiently inserted by a bimolecular donor reaction into a supercoiled DNA target (2867 bp ), producing the HlV-1 5-bp host site duplication. Sequence data were analyzed from 193 donor-target recombinants obtained from the linear 3 .8-kb DNA product. The selection of host target sites appeared randoml y distributed and was independent of lysis and assay conditions. The f idelity of the 5-bp duplications in comparison to other size duplicati ons was highest (94%) with high-salt (300 mM NaCl) lysis of the virion s and 60 mM NaCl for strand transfer using Mg2+ as the divalent cation . Base sequence analysis demonstrated some biases in the 5-bp duplicat ions at the sites of strand transfer and at the immediate host sequenc es surrounding the duplications. In addition to the observed duplicati ons, similar to 30% of the recombinants isolated from the linear 3.8-k b DNA product contained specific and repetitive small-size deletions. No deletions smaller that 17 bp were observed and the distance between the deletion sets had a periodicity of similar to 10 bp. The mechanis ms involved in how HIV-1 IN produces the 5-bp duplications and the rep etitive host site deletions are discussed. (C) 1997 academic Press.