Host site selection for concerted integration by human immunodeficiency virus type-1 virions in vitro.
Host site selection for full-site integration by human immunodeficiency virus type-1 (HIV-1) intergrase (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 mM NaCl) lysis of the virions and 60 mM NaCl 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, approximately 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 approximately 10 bp. The mechanisms involved in how HIV-1 IN produces the 5-bp duplications and the repetitive host site deletions are discussed.
Goodarzi
G
G
Institute for Molecular Virology, St. Louis University Health Sciences Center, Missouri 63110, USA.
Chiu
R
R
Brackmann
K
K
Kohn
K
K
Pommier
Y
Y
Grandgenett
D P
DP
D002478:Cells, Cultured; D004278:DNA, Superhelical; D003902:Detergents; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D010957:Plasmids; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D017384:Sequence Deletion; D014771:Virion / Q000737:chemistry / Q000235:genetics*; D016662:Virus Integration
D004278:DNA, Superhelical; D003902:Detergents