Host Site Selection for Concerted Integration by Human Immunodeficiency Virus Type-1 Virionsin Vitro

• Published in: Virology (New York, N.Y.) N.Y.), 1997-05, Vol.231 (2), p.210-217
• Main Authors: Goodarzi, Goodarz, Chiu, Roger, Brackmann, Karl, Kohn, Kurt, Pommier, Yves, Grandgenett, Duane P.
• Format: Article
• Language: English
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1006/viro.1997.8558

Host site selection for full-site integration by human immunodeficiency virus type-1 (HIV-1) integrase (IN) from nonionic detergent-lysed virions was investigated. Linear retrovirus-like DNA (469 bp) possessing 3′ OH recessed long terminal repeat termini was efficiently inserted by a bimolecular donor reaction into a supercoiled DNA target (2867 bp), producing the HIV-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 randomly distributed and was independent of lysis and assay conditions. The fidelity of the 5-bp duplications in comparison to other size duplications was highest (94%) with high-salt (300 mMNaCl) lysis of the virions and 60 mMNaCl for strand transfer using Mg2+as the divalent cation. Base sequence analysis demonstrated some biases in the 5-bp duplications at the sites of strand transfer and at the immediate host sequences surrounding the duplications. In addition to the observed duplications, ∼30% of the recombinants isolated from the linear 3.8-kb 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 ∼10 bp. The mechanisms involved in how HIV-1 IN produces the 5-bp duplications and the repetitive host site deletions are discussed.